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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
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Change or document AR_compound low scoring compound penalty #107

Open dnil opened 1 year ago

dnil commented 1 year ago

The hard coded -6 rank score penalty incurred by AR_comps with only low scoring (arbitrarily hard coded as score 9) variants is not reflected in the rankResults string exported explaining the rank results. It would not hurt to 1) figure out a way to solve the signal-noise of AR_comp without this penalty - it hits very differently in singletons vs trios 2) make it a part of the score model 3) make it appear in the rankResults.

dnil commented 1 week ago

One more case of this https://scout.scilifelab.se/cust002/F0060093/6f7843d6fe355b956031e6aa5664bad7 from @AnnHamm. In general it is a weakness of the scoring model, and fixing it will allow analysts to "stop" searching at a higher score, giving shorter analysis time. Most false negatives among singletons for score thresholds were found to be caused by this particular flag. A recalibration of trio scores will be needed after changing it, but perhaps not dramatically as AR_comp is a very common occurrence in singletons.